scholarly journals Precise Estimation of In Vivo Protein Turnover Rates

2020 ◽  
Author(s):  
Jonathon J. O’Brien ◽  
Vikram Narayan ◽  
Yao Wong ◽  
Phillip Seitzer ◽  
Celeste M. Sandoval ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Turnover ◽  
Search Algorithm ◽  
Deuterium Oxide ◽  
Isotopic Labeling ◽  
Analytical Framework ◽  
Turnover Rates ◽  
Ion Distribution ◽  
Common Technique

AbstractIsotopic labeling with deuterium oxide (D2O) is a common technique for estimating in vivo protein turnover, but its use has been limited by two long-standing problems: (1) identifying non-monoisotopic peptides; and (2) estimating protein turnover rates in the presence of dynamic amino acid enrichment. In this paper, we present a novel experimental and analytical framework for solving these two problems. Peptides with high probabilities of labeling in many amino acids present fragmentation spectra that frequently do not match the theoretical spectra used in standard identification algorithms. We resolve this difficulty using a modified search algorithm we call Conditional Ion Distribution Search (CIDS). Increased identifications from CIDS along with direct measurement of amino acid enrichment and statistical modeling that accounts for heterogeneous information across peptides, dramatically improves the accuracy and precision of half-life estimates. We benchmark the approach in cells, where near-complete labeling is possible, and conduct an in vivo experiment revealing, for the first time, differences in protein turnover between mice and naked mole-rats commensurate with their disparate longevity.

scholarly journals A New Technic for the Production of an in Vivo Labeled Fibrinogen

Blood ◽  
1967 ◽  
Vol 29 (4) ◽  
pp. 517-525 ◽  
Author(s):  
HENRY GANS ◽  
JAMES MC LEOD ◽  
JAMES T. LOWMAN
Keyword(s):  
Amino Acid ◽  
Specific Activity ◽  
High Specific Activity ◽  
Entire Period ◽  
Turnover Rates ◽  
Prolonged Infusion ◽  
Slow Infusion

Abstract The fact that in vitro labeled proteins, as a rule, exhibit faster turnover rates than in vivo labeled materials led us to explore means of obtaining in vivo labeled fibrinogen of high specific activity. It was found that defibrination of the rat provides a stimulus for the liver to regenerate fibrinogen at an accelerated rate. Administration of seleno75 methionine shortly after thrombin-induced defibrination of the animal resulted in the incorporation of large quantities of the label. The rate of incorporation was further increased if the amino acid was administered as a slow infusion during the entire period of fibrinogen regeneration. In addition, prior nephrectomy of the animal would appear to result in a slight increase in specific activity of the fibrinogen preparation obtained. The results of these studies indicate that defibrination, nephrectomy, and the prolonged infusion of the labeled amino acid selenomethionine provided us with a technic for obtaining a biosynthetically labeled, γ-emitting, fibrinogen preparation of high specific activity.

scholarly journals PROTEIN METABOLISM IN TUMOR CELLS AT VARIOUS STAGES OF GROWTH IN VIVO

1974 ◽  
Vol 62 (3) ◽  
pp. 585-593 ◽  
Author(s):  
Massimo Olivotto ◽  
Francesco Paoletti
Keyword(s):  
Protein Synthesis ◽  
Amino Acid ◽  
Tumor Cells ◽  
Protein Metabolism ◽  
Protein Turnover ◽  
Specific Activity ◽  
Cell Mass ◽  
Ascites Hepatoma ◽  
Two Phases

Protein metabolism of Yoshida ascites hepatoma cells was studied in the early phase of logarithmic proliferation and in the following stage in which cell mass remains constant (resting phase). The rate of protein synthesis was measured by a short-time incorporation of [8H]lysine, while degradation was concurrently assessed by following the decrease of specific activity of [14C]lysine-labeled proteins. Most of the labeled amino acid injected intraperitoneally into the animal was immediately available for the tumor cells, with only a minor loss towards the extra-ascitic compartment. It was thus possible to calculate the dilution of the isotope in the ascitic pool of the lysine, which increased concurrently with the ascitic plasma volume. Amino acid transport capacity did not change in the log vs. the resting cells. This fact permitted the correction of the specific activity of the proteins synthesized by tumors in the two phases, taking into account the dilution effect. Protein synthesis was found to proceed at a constant rate throughout each of the two phases, although it was 30% lower during the resting as compared to the log phase. When cell mass attained the steady-state, protein degradation occurred at such a level as to balance the synthesis. Throughout the resting phase the amount of lysine taken up by the cells and renewed from the blood remained unchanged. Protein turnover, as studied in subcellular fractions, exhibited a similar rate in nuclei and microsomes, where it proceeded at a higher level than in mitochondria. On the whole, the results encourage the use of the Yoshida ascites hepatoma as a suitable model for studying protein turnover in relation to cell growth in vivo.

In vivo amino acid metabolism of gut and liver during short and prolonged starvation

1996 ◽  
Vol 270 (2) ◽  
pp. G298-G306 ◽  
Author(s):  
I. de Blaauw ◽  
N. E. Deutz ◽  
M. F. Von Meyenfeldt
Keyword(s):  
Amino Acid ◽  
Membrane Transport ◽  
Protein Turnover ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Muscle Membrane ◽  
Liver Protein ◽  
Protein Loss ◽  
Prolonged Starvation

During starvation, splanchnic organs are proportionally more affected by protein loss than other organs. Amino acid membrane transport is one of the regulating mechanisms of protein turnover, but until now in vivo data were lacking. To study in vivo phenylalanine and tyrosine membrane transport and protein turnover in splanchnic organs, a primed continuous infusion of L-[2,6-3H]phenylalanine was given to control rats (postabsorptive) and after short (40 h) and prolonged (112 h) starvation. Data were analyzed using a three-compartment model previously used in muscle membrane transport studies. Inward and outward amino acid plasma-tissue membrane transport rates in both the liver and gut were upregulated after prolonged starvation. Metabolic shunting of phenylalanine and tyrosine increased in the gut but decreased to zero in the liver after prolonged starvation. In conjunction with this, gut and liver protein turnover increased after prolonged starvation. In the liver the net uptake of gluconeogenic precursors also increased, indicative for increased gluconeogenesis. The observed changes in amino acid metabolism in both splanchnic organs after prolonged starvation may reflect an adaptation of the gut and liver to nutritional deprivation and could be of benefit during refeeding.

The N-end rule of selective protein turnover and its implications [abstract only]

1987 ◽  
Vol 317 (1187) ◽  
pp. 471-471
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acids ◽  
Amino Acid ◽  
Fusion Protein ◽  
Protein Turnover ◽  
Secreted Proteins ◽  
Gene Encoding ◽  
Intracellular Proteins ◽  
N Terminus

When a chimeric gene encoding a ubiquitin: β-galactosidase fusion protein is expressed in the yeast Saccharomyces cerevisiae , ubiquitin is efficiently cleaved off the nascent fusion protein, yielding a deubiquitinated β-galactosidase (βgal). With one exception, this cleavage takes place irrespective of the nature of the amino acid residue of βgal at the ubiquitin-βgal junction. This result, in effect, allows one to expose different residues at the N-termini of the otherwise identical βgal proteins produced in vivo . The βgal proteins thus designed exhibit a striking diversity of in vivo half-lives, from more than 10h to less than 3 min, depending on the nature of the amino acid exposed at the N-terminus of βgal. The N-terminal location of an amino acid is essential for its effect on βgal half-life. The set of individual amino acids can thus be ordered with respect to the half-lives that they confer on βgal when present at its N-terminus (the ‘N-end rule’). The known N-terminal residues in long-lived intracellular proteins from both prokaryotes and eukaryotes are exclusively of the stabilizing class as predicted by the N-end rule. In contrast, a majority of the N-terminal residues in compartmentalized (e.g. secreted) proteins are of the destabilizing class. The N-end rule may thus underlie both the diversity of protein half-lives in vivo and the selective destruction of otherwise normal but miscompartmentalized proteins. The N-end may also account for the function of the previously described post-translational addition of single amino acids to protein N-termini. Thus the recognition of an N-terminal residue in a protein may mediate both the metabolic stability of the protein and the potential for regulation of its stability.

scholarly journals The number of catalytic cycles in an enzyme’s lifetime and why it matters to metabolic engineering

2021 ◽  
Vol 118 (13) ◽  
pp. e2023348118
Author(s):  
Andrew D. Hanson ◽  
Donald R. McCarty ◽  
Christopher S. Henry ◽  
Xiaochen Xian ◽  
Jaya Joshi ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Active Site ◽  
Protein Turnover ◽  
Metabolic Flux ◽  
Failure Modes ◽  
High Energy ◽  
Enzyme Engineering ◽  
Turnover Rates ◽  
Catalytic Cycles

Metabolic engineering uses enzymes as parts to build biosystems for specified tasks. Although a part’s working life and failure modes are key engineering performance indicators, this is not yet so in metabolic engineering because it is not known how long enzymes remain functional in vivo or whether cumulative deterioration (wear-out), sudden random failure, or other causes drive replacement. Consequently, enzymes cannot be engineered to extend life and cut the high energy costs of replacement. Guided by catalyst engineering, we adopted catalytic cycles until replacement (CCR) as a metric for enzyme functional life span in vivo. CCR is the number of catalytic cycles that an enzyme mediates in vivo before failure or replacement, i.e., metabolic flux rate/protein turnover rate. We used estimated fluxes and measured protein turnover rates to calculate CCRs for ∼100–200 enzymes each from Lactococcus lactis, yeast, and Arabidopsis. CCRs in these organisms had similar ranges (<103 to >107) but different median values (3–4 × 104 in L. lactis and yeast versus 4 × 105 in Arabidopsis). In all organisms, enzymes whose substrates, products, or mechanisms can attack reactive amino acid residues had significantly lower median CCR values than other enzymes. Taken with literature on mechanism-based inactivation, the latter finding supports the proposal that 1) random active-site damage by reaction chemistry is an important cause of enzyme failure, and 2) reactive noncatalytic residues in the active-site region are likely contributors to damage susceptibility. Enzyme engineering to raise CCRs and lower replacement costs may thus be both beneficial and feasible.

A mass spectrometry workflow for measuring protein turnover rates in vivo

2019 ◽  
Vol 14 (12) ◽  
pp. 3333-3365 ◽  
Author(s):  
Mihai Alevra ◽  
Sunit Mandad ◽  
Till Ischebeck ◽  
Henning Urlaub ◽  
Silvio O. Rizzoli ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Turnover ◽  
Turnover Rates

Plasma amino acid turnover rates and pools in rabbits: in vivo studies using stable isotopes.

1979 ◽  
Vol 237 (5) ◽  
pp. E418 ◽  
Author(s):  
I Nissim ◽  
A Lapidot
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
In Vivo Studies ◽  
Whole Body ◽  
Gas Chromatography Mass Spectrometry ◽  
Plasma Amino Acids ◽  
Isotope Enrichment ◽  
Time Decay ◽  
Turnover Rates

Gas chromatography--mass spectrometry of plasma amino acids has been used to determine the 15N enrichments of plasma glycine and alanine in rabbits in different metabolic states. Isotope-enrichment time-decay curves of plasma amino acids were linear over the course of the measurements after intravenous administration of a single dose of 15N-amino acid. Glycine and alanine pools and turnover rate constants were estimated from decay data. The effects of diurnal variation and fasting on glycine and alanine pool sizes, turnover rates, and flux in rabbits were studied to provide information on the effect of metabolic stress on amino acid kinetics in the whole body. The observations suggests that the transport of systemic glycine or alanine into the hepatocyte is under the control of a regulatory mechanism that compensates for decrease in the extracellular levels of the amino acids by enhancing the activity of the transport system. The volumes of the glycine and alanine pools were found to correspond to the extracellular space of rabbits, and the glycine and alanine pools can be identified as extracellular. We conclude that the plasma glycine and alanine 15N isotope-enrichment time-decay curves over the 1st h after a single intravenous dose of the amino acid represent mainly the hepatic uptake of glycine and alanine from the extracellular pool.

Aminoacyl-tRNA and tissue free amino acid pools are equilibrated after a flooding dose of phenylalanine

1999 ◽  
Vol 277 (1) ◽  
pp. E103-E109 ◽  
Author(s):  
Teresa A. Davis ◽  
Marta L. Fiorotto ◽  
Hanh V. Nguyen ◽  
Douglas G. Burrin
Keyword(s):  
Skeletal Muscle ◽  
Protein Synthesis ◽  
Amino Acid ◽  
Free Amino Acid ◽  
Free Amino ◽  
Specific Radioactivity ◽  
Isotopic Labeling ◽  
Precursor Pool ◽  
Free Amino Acid Pools

The flooding dose method, which is used to measure tissue protein synthesis, assumes equilibration of the isotopic labeling between the aminoacyl-tRNA pool and the tissue and blood free amino acid pools. However, this has not been verified for a phenylalanine tracer in an in vivo study. We determined the specific radioactivity of [3H]phenylalanine in the aminoacyl-tRNA and the tissue and blood free amino acid pools of skeletal muscle and liver 30 min after administration of a flooding dose of phenylalanine along with [3H]phenylalanine. Studies were performed in neonatal pigs in the fasted and refed states and during hyperinsulinemic-euglycemic-amino acid clamps. The results showed that, 30 min after the administration of a flooding dose of phenylalanine, there was equilibration of the specific radioactivity of phenylalanine among the blood, tissue, and tRNA precursor pools. Equilibration of the specific radioactivity of the three precursor pools for protein synthesis occurred in both skeletal muscle and liver. Neither feeding nor insulin status affected the aminoacyl-tRNA specific radioactivity relative to the tissue free amino acid specific radioactivity. The results support the assumption that the tissue free amino acid pool specific radioactivity is a valid measure of the precursor pool specific radioactivity and thus can be used to calculate protein synthesis rates in skeletal muscle and liver when a flooding dose of phenylalanine is administered.

scholarly journals The oxidation of leucine in tumour-bearing rats

1990 ◽  
Vol 268 (1) ◽  
pp. 241-244 ◽  
Author(s):  
J M Argilés ◽  
F J López-Soriano
Keyword(s):  
Amino Acid ◽  
Time Course ◽  
Similar Rate ◽  
Turnover Rates ◽  
Tissue Slices ◽  
Tracer Dose ◽  
Tumour Bearing ◽  
Walker 256 ◽  
14Co2 Release

Rats bearing the Walker-256 carcinosarcoma showed significant changes in leucine metabolism compared with their non-tumour-bearing controls. After a single intravenous tracer dose of L-[1-14C]leucine in vivo, 14CO2 release by tumour-bearing rats was significantly elevated throughout the time course of administration. In addition, both the clearance and turnover rates of the tracer were significantly enhanced in these animals. Incubation of soleus muscles from control and tumour-bearing rats in the presence of L-[1-14C]leucine revealed an enhanced oxidation of the amino acid in the tumour-bearing group. Tumour tissue slices were also able to oxidize the tracer at a similar rate to that found in soleus muscles from control animals.

scholarly journals Protein turnover and growth in the whole body, liver and kidney of the rat from the foetus to senility

1984 ◽  
Vol 217 (2) ◽  
pp. 507-516 ◽  
Author(s):  
D F Goldspink ◽  
F J Kelly
Keyword(s):  
Protein Synthesis ◽  
Protein Turnover ◽  
Post Partum ◽  
Protein Composition ◽  
Whole Body ◽  
Turnover Rates ◽  
Tissue Mass ◽  
Age Related ◽  
Foetal Life

Changes in the growth and protein turnover (measured in vivo) of the rat liver, kidney and whole body were studied between 16 days of life in utero and 105 weeks post partum. Tissue and whole-body growth were related to changes in both cellular hyperplasia (i.e. changes in DNA) and hypertrophy (protein/DNA values) and to the protein composition within the enlarging tissue mass. The suitability of using a single large dose of phenylalanine for measuring the rates of protein synthesis during both pre- and post-natal life was established. The declining growth rates in the whole animal and the two visceral tissues were then explained by developmental changes in the fractional rates of protein synthesis and breakdown, turnover rates being age-for-age higher in the liver than in the kidney, which in turn were higher than those measured in the whole animal. The declining fractional rates of synthesis in both tissues and the whole body with increasing age were related to changes in the tissues' ribosomal capacity and activity. The fall in the hepatic rate between 18 and 20 days of foetal life (from 134 to 98% per day) corresponded to a decrease in both the ribosomal capacity and the rate of synthesis per ribosome. No significant changes in any of these parameters were, however, found in the liver between weaning (3 weeks) and senility (105 weeks). In contrast, the fractional synthetic (and degradative) rates progressively declined in the kidney (from 95 to 24% per day) and whole body (from 70 to 11% per day) throughout both pre- and post-natal life, mainly as a consequence of a progressive decline in the ribosomal capacity, but with some fall in the ribosomal activity also during foetal life. The age-related contributions of these visceral tissues to the total amount of protein synthesized per day by the whole animal were determined. The renal contribution remained fairly constant at 1.6-2.9%, whereas the hepatic contribution declined from 56 to 11%, with increasing age. Approximate-steady-state conditions were reached at, and between, 44 and 105 weeks post partum, the half-life values of mixed whole-body, kidney and liver proteins being 6.4, 3.0 and 1.5 days, respectively, at 105 weeks.

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